Mountains, Lakes, and Ancient Drainage Networks Sculpt the Phylogeographic Architecture of the Stream Headwater Fish Acrossocheilus kreyenbergii in China

Background: Phylogeographic surveys of obligate freshwater fishes could serve as a pivotal lens through which the biological footprints of historic drainage rearrangements can be deciphered. Methods: Focusing on the headwater-restricted cyprinid Acrossocheilus kreyenbergii in the Pearl, Yangtze, and Huai river basins, we examined variations in mitochondrial cytochrome b gene (Cyt b) to elucidate the phylogeographic architecture and evolutionary history of this stream fish in South–Central China through integrative analyses of phylogeny, ancestral area reconstruction, genetic structure, and population demography. Results: A time-calibrated phylogeny recovered two primary lineages, K-I and K-II, which diverged ca. 2.15 Ma: K-I split into K-Ia (Huai River) and K-Ib (Yangtze–Poyang Lake catchment) at 1.53 Ma, whereas K-II gave rise to K-IIa, K-IIb, and K-IIc through sequential divergences at 1.29 Ma and 0.83 Ma, with K-IIa restricted to the Poyang Lake catchment. K-IIb was shared between the Poyang Lake catchment and the Qiupu River (Yangtze basin), and K-IIc was distributed in the Xijiang River (Pearl basin) as well as the Yangtze–Dongting Lake catchment. Conclusions: Our findings reveal that the phylogeographic architecture of A. kreyenbergii was sculpted by a succession of geologic and anthropocentric events: the Late-Cenozoic collapse of the Zhe–Min Uplift first fractured its range; the intervening Mufu–Lianyun–Luoxiao Mountains then acted as a persistent barrier; the large waters of Poyang and Dongting Lakes served as biological filters; and the 2200-year-old Lingqu Canal—constructed during the Qin dynasty—briefly re-established a corridor for gene flow. Together, these forces disrupted and reorganized the species’ genetic connections, leaving a visible imprint today.